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Yorodumi- PDB-1i27: CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 SUBUNIT O... -
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-Basic information
Entry | Database: PDB / ID: 1i27 | ||||||
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Title | CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 SUBUNIT OF HUMAN TRANSCRIPTION FACTOR IIF (TFIIF) | ||||||
Components | TRANSCRIPTION FACTOR IIF | ||||||
Keywords | TRANSCRIPTION / GENERAL TRANSCRIPTION FACTOR / RAP74 / RAP30 / TFIIF / RNA POLYMERASE II / WINGED-HELIX DOMAIN | ||||||
Function / homology | Function and homology information phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / negative regulation of protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / response to virus / cell junction / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / intracellular membrane-bounded organelle / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.02 Å | ||||||
Authors | Kamada, K. / De Angelis, J. / Roeder, R.G. / Burley, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF. Authors: Kamada, K. / De Angelis, J. / Roeder, R.G. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i27.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i27.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i27_validation.pdf.gz | 360.6 KB | Display | wwPDB validaton report |
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Full document | 1i27_full_validation.pdf.gz | 361.1 KB | Display | |
Data in XML | 1i27_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 1i27_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/1i27 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/1i27 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8374.801 Da / Num. of mol.: 1 / Fragment: RAP74 SUBUNIT, C-TERMINAL DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAP74 / Plasmid: PGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35269 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Zinc Sulfate, Lithium chloride, PEG 2000 MME, polyvinylpyrrolidone 15K, glucosamine hydrochloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 |
Detector | Type: SBC-2 / Detector: CCD / Date: Jul 2, 2000 / Details: VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→20 Å / Num. obs: 58701 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.02→1.06 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.335 / Rsym value: 0.335 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.02→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.02→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.126 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |